Mandrake

Mandrake performs dimensional reduction and embedding of microbial genomic datasets, including millions of whole genomes, to visualize population structure and genetic diversity in population genomics studies.

Key Features:

• Dimensional Reduction Methodology: Mandrake employs an efficient implementation of dimensional reduction techniques tailored for large-scale population genomics to transform complex genomic datasets into low-dimensional representations.
• Data Modalities Compatibility: Mandrake processes multiple sequence alignments, genome assemblies, and gene content estimates across genomes.
• Visualization of Population Structure: Mandrake embeds genomic data into low-dimensional spaces to enable rapid exploration and visualization of microbial population structures.
• Application to Major Pathogens: Mandrake has been applied to datasets representing major pathogens to support analyses of pathogen evolution and spread.

Scientific Applications:

• Epidemiology: Mandrake elucidates genetic relationships and diversity among pathogen strains to aid outbreak tracking and transmission inference.
• Evolutionary Biology: Mandrake supports study of evolutionary patterns within microbial populations, informing analyses of adaptation and speciation.
• Genomic Surveillance: Mandrake enables rapid assessment of population genomics data for genomic surveillance and public health response.

Methodology:

Efficient implementation of dimensional reduction techniques that embed multiple sequence alignments, genome assemblies, and gene content estimates into a low-dimensional space for visualization of population structure.